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APC Superfamily
The amino acid/polyamine/organocation (APC) superfamily is among the largest transport superfamilies identified. It is found in all forms of life. However, not much is known about the structures of members of this family, because not many proteins have been crystallized. These few structures lend much insight into the qualities of the superfamily as a whole when compared with existing hydropathy plots and other structural studies.

Superfamilies have been identified using phylogenetic analysis. Thus, only proteins with similar genetic qualities and evolutionary roots are considered members of the same superfamily. Because of this, proteins with similar topographies are not necessarily in the same superfamily. For instance, the core structures of ApcT and AdiC, members of the APC superfamily discussed below, are very similar to that of LeuT (a member of the neurotransmitter sodium symporter (NSS) family), BetP (a member of the betaine/chlorine/carnitine transporter (BCCT) family), vSGLT (of the solute sodium symporter (SSS) family) and Mhb1 (of the nucleobase-cation-symport-1 (NCS1) family)

Various structural studies have been conducted outside of crystallography. According to hydropathy plots, all members of the APC superfamily exhibit a uniform topology formed by a single polypeptide chain that crosses the plasma membrane 12 times, unless otherwise noted. All of these proteins also share a similar structural core, consisting of two V-shaped domains of five transmembrane domains each, intertwined in an antiparallel topology. Each protein's N- and C-termini are located in the cytosol. The loops in the cytosol tend to be smaller than the loops located in the extracellular space. The smaller proteins are generally of prokaryotic origin, whereas the larger ones are of eukaryotic origin and have N- and C-terminal hydrophilic extensions.

Functional studies have revealed that some proteins in this superfamily exhibit broad specificity while others respond to only one or a few substrates.

ApcT - a proton-coupled amino acid transporter
ApcT has not been placed in a particular family within the APC superfamily. It is a proton-coupled amino acid transporter.

  Here, you can see the directionality of the protein where the N-terminus is gradually shaded into the C-terminus according to the scale below.

ApcT is cylindrical in shape with 12 TM domains (numbered from N-terminus to C-terminus), short intracellular and extracellular loops, and each termini ending in the cytoplasm, consistent with the topography of AdiC described below.

ApcT is a proton-coupled, broad specificity transporter. It transports a range of amino acids (Glu, Ala, > Ser, Gln > Phe,) but transports the smallest (Gly) or largest (Trp) amino acids very slowly, if at all.

Lys-158, shown here in pink, has been proposed to be necessary for proton coupled transport in this protein. Because the displayed structure was collected in alkaline conditions, it is assumed that this is the conformation of the protein when Lys-158 is not protonated. Upon protonation of the Lys-158 amine group, it is expected that ApcT will isomerize from this inward facing state to an outward facing conformation, ready to bind the substrate and return to an inward facing conformation to release/exchange it. Experiments with ApcT established that the occluded formation, a formation in which the substrate binding pocket is protected from the protein's environment, is not dependent on substrate binding.

AAT: Amino Acid Transporter
Unique to bacteria, this is the largest family within the APC superfamily. Members of this family have short hydrophilic extensions at both termini. One example of a protein in this family is GabP, a γ-Aminobutyrate permease isolated from both Bacillus subtilis and Escherichia coli. GabP appears to follow the APC topography of 12TMs and cytoplasmic termini, based on hydropathy and experimental analysis.

APA: Basic Amino Acid/Polyamine Transporter
The APA family is also unique to bacteria. For example, ArcD, an arginine:orithine transporter has been identified in Chlamydophilia pneumoniae and Chlamydia trachomatis.

AdiC - an example from the APA family
AdiC has been determined to be a member of the APC superfamily through phylogenetic analysis.

AdiC is a representative member of the APC superfamily; it contains 12 TMs with each termini located in the cytosol. AdiC functions as an arginine/agmatine antiporter in E. coli, Salmonella enterica serovar Typhimurium, and other bacteria when the cell is exposed to acidic environments. Agmatine is the product of arginine decarboxylation. An associated protein, AdiA, is thought to decarboxylate arginine molecules for transport. By exchanging intracellular agmatine (Agm(2+)) for extracellular arginine (Arg(+)), AdiC removes virtual protons from the interior of the cell, enabling the bacteria to survive in acidic conditions by preventing acidification of the cytosol.

 Though the structure is shown as a homodimer, each subunit is an independently functioning transporter. Here, half the homodimer, one functioning subunit, is labelled to show directionality of the polypeptide. As in ApcT, 10 of the transmembrane helices surround the pore in antiparallel fashion, with TM1 paired with TM6, TM2 with TM7, and so on. TMs 11 and 12 do not participate in this pairing scheme; instead, they form most of the homodimeric interface. TMs 1 and 6 contain short, non-helical, Gly-containing loops midway across the membrane, thought to be important for substrate interactions. Amino acids in these loops are highly conserved within distinct families of the APC superfamily. For example, AdiC, CadB, and PotE, which all belong to the APA family, share two signature loop sequences, the GSG motif (Gly25-Ser26-Gly27) in TM1 and the GVESA motif (Gly206-Val-Glu-Ser-Ala210) in TM6.

 Arg binding induces a structural rearrangement in TM6 and minor changes in TM2 and TM10, resulting in an occluded formation. Trp-293 has been demonstrated to be vital for substrate recognition. Trp-293 is buried in the substrate-binding site, shown here in purple wire frame representation. Notice the aromatic interactions with the substrate. Tyr-93 is another residue proposed to be vital for substrate specificty and/or binding,  shown here in green wire frame. Trp-293 and Tyr-93 come from TM8 and TM3, respectively. Glu-208 displayed in orange also appears to have a role in regulating the upload and release of substrate by acting as a pH sensor. In the stomach (pH 2-3), Glu-208 (pKa approx 4.25) is likely protonated while other residues with a pKa of approx 2 are mostly unprotonated. Thus, the majority of these amino acids carry no net charge on their head groups, with the positively charged a-amino group offsetting the negatively charged a-carboxyl group. Protonated Glu-208 likely binds to the neutral head groups of the substrate amino acid (arginine). Once facing the intracellular environment (pH 4-5), Glu-208 is likely to deprotonate, developing a net negative charge in the substrate-binding cavity. The negative charge may attract positively charged head group of the a-decarboxylated amino acid (agmatine) and favor its binding. When this occurs, agmatine replaces arginine in the binding site, releasing arginine into the cytosol and initiating the deportation of the agmatine.

CAT: Cationic Amino Acid Transporter
Members of the CAT family are ubiquitous, containing 14 TMs in eukaryotes and 12 TMs in prokaryotes. These proteins have short, hydrophilic, N-terminal extensions. CAT2 provides arginine for NO synthesis and arginase in classical and alternative activation of macrophages. CAT1 is required for macrophage proliferation. Members of this family have been shown to serve as viral receptors in animals.

ACT: Amino Acid/Choline Transporter
Members of the ACT family can be found in yeast, plants, and fungi. These proteins have short hydrophilic extensions at the C and N termini.

EAT: Ethanolamine Transporter
Members of the EAT family are found in bacteria. They have no noticeable extensions beyond the 12 TMs. Ethanolamine permeases from this family have been identified in both Rhodococcus erythropolis - a bacterium found in crude oil, and Zymomonas mobilis.

ABT: Archaeal/Bacterial Transporter
As the name suggests, members of the ABT family are found in archaea and bacteria. One member (Cat1 Afu) of this family exhibits a long, C-terminal extension that may function in interactions with other proteins.

GGA: Glutamate:GABA Antiporter
Members of the GGA family are found only in bacteria. There proteins have short, hydrophilic, N-terminal extensions.

LAT: L-type Amino Acid Transporter
Members of the LAT family have been identified in animals and yeast. The LAT proteins correspond to the light chains in heteromeric amino acid transporters (HATs) in eukaryotes. A HAT is composed of two subunits: one membrane protein (the light subunit) and a disulfide-linked N-glycosylated type II membrane glycoprotein (the heavy subunit). The light subunit is the catalytic component of the transporter, whereas the heavy subunit appears to be vital only for trafficking substrates to the plasma membrane.

LAT1 has been found to be overexpressed in a wide variety of primary human cancer and is important to cell growth and survival in cancer cell lines.

SteT - an example from the LAT family
SteT (Serine/Threonine antiporter) from Bacillus subtilis is the first characterized prokaryotic member of the LAT family, put into this family by phylogenetic analysis. Transmission electron microscopy revealed elliptical particles (diameters 6 × 7 nm) with a distinct central depression. Comparing the apparent structure of SteT with that of AdiC and ApcT as well as performing functional analysis through mutagenesis studies suggests the involvement of different TM8 residues in substrate binding and translocation in the LAT transporter SteT: The large change in the amino acid substrate specificity of SteT as a result of single mutations in residue Lys-295 demonstrates the plasticity of the substrate binding site of the LAT family (and the APC superfamily). TM1, TM2, and the re-entrant loop between TM2 and TM3 were found to be conserved between the prokaryotic SteT and eukaryotic LAT family members.
 * Cys-291 (structurally equivalent to Ser-289 in AdiC) is close to the substrate binding site and possibly directly interacts with the substrate L-Serine.
 * Lys-295 (equivalent to Trp-293 in AdiC) is a determinant of substrate selectivity.
 * S-thiolation of Gly-294 (equivalent to Gly-292 in AdiC) blocks substrate translocation.

SPG: Spore Germination Protein
Members of this family are found in prokaryotes and exhibit only 10 transmembrane segments. The 2 segments closest to the C-terminus in other members of this super family appear to have been cleaved when this family was evolving. None of the proteins in this family have been identified as transporters, leading to the possibility that transmembrane segments 11 and 12 are vital for transport function.

YAT: Yeast Amino Acid Transporter
Members of the YAT family have been identified in both yeast and fungi. Some members of this family exhibit long, N-terminal, hydrophilic extensions beyond the 12 TMs. Examples of this family include lysine-specific permease, proline-specific permease, and tryptophan permease all isolated from Saccharomyces cerevisiae. Another amino acid transporter (Aat1 Amu) isolated from Amanita muscaria also belongs to the YAT family.